BacGrid: LARGE SCALE SYSTEMS BIOLOGY SIMULATION ON THE GRID

Modelling and simulation form an integral part of a predictive and explanatory approach to computational systems biology. However, systems biology simulations are extremely challenging in requiring the modelling of many complex phenomena at multiple spatial and temporal scales. No single simulation can cover all the cases of interest. As a result, simulations must be developed “on demand” to suit each new systems biology problem, often drawing on the expertise of different research groups. Such large scale collaborative model development presents significant challenges for the distributed simulation community. We believe these challenges can potentially be met by a combination of two emerging standards and their supporting middleware: the Grid and the High Level Architecture. The Grid supports e-Science through resource discovery, secure access to remote computational resources, data archiving and sharing etc., allowing virtual research teams to collaborate to solve research problems. The High Level Architecture (HLA) is an IEEE standard (IEEE 2000) for simulator interoperability, which supports the creation of distributed, composable simulations. The combination of these two complementary technologies offers great promise for the “on-demand” development of systems biology simulations by facilitating the reuse of existing simulation components. In addition, many of the services necessary to support dynamic composition of simulations, e.g., model discovery and matching, secure execution, migration and load balancing, sharing and archival of simulation results etc., which are not addressed by the HLA standard, can potentially be provided by the Grid infrastructure. In recent work, some initial steps have been taken towards the composition and subsequent execution of simulation models on the Grid, e.g., HLA_Grid (Xie et al. 2005), XMSF (Pullen et al. 2005). However this work is still relatively immature and the appropriateness of the HLA for biological simulation has yet to be established. To evaluate the suitability of the HLA as a standard for systems biology simulations on the Grid, we are developing a prototype HLAcompliant, Grid-based simulator for systems biology which we call BacGrid. In this abstract, we outline the systems biology problem we have adopted as a test case, briefly describe the simulation model and the architecture of the simulator and summarise the current state of the implementation.